further fix around array allocation for SETTLE

patch settle to allow use OpenMP for unallocated velocities

further cleanup of documentation and Tinker manual

update to Tinker 25.6; add SETTLE constraints for water

provide support for the RCSB PDBx/mmCIF file format

fix output formatting in TESTSURF surface/volume checker

assign atoms to default group 0 when groups are not specified

correct removal of inertia during MD for default group

comment changes for GitHub release of Tinker 25.5

add VRESPA and BRESPA options for MTS MD integrators